VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens

Wang, Meng; Goh, Ying-Xian; Tai, Cui; Wang, Hui; Deng, Zixin; Ou, Hong‐Yu

doi:10.1093/nar/gkac321

Cited by 64 publications

(42 citation statements)

References 30 publications

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“…However, CHP cannot be retrieved from the bacterial mobile genetic elements database (mobileOG and VRprofile2) by domain or sequence similarity. 31 , 32 For class D β-lactamases, most were identified in the chromosome as an intrinsic resistance determinant, while only a few were found in mobile genetic elements. 26 , 30 The bla RAD-1 gene reported in this study was located chromosomally and distributed widely in R. anatipestifer.…”

Section: Resultsmentioning

confidence: 99%

Identification of a novel carbapenem-hydrolysing class D β-lactamase RAD-1 inRiemerella anatipestifer

Yang

Lei

et al. 2023

Journal of Antimicrobial Chemotherapy

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Objectives To elucidate the role of a novel carbapenem-hydrolysing class D β-lactamase (RAD-1) from Riemerella anatipestifer. Methods We applied WGS and bioinformatic analysis to screen putative β-lactamase genes in R. anatipestifer SCVM0004. A putative class D β-lactamase gene was cloned into pET24a and transferred into Escherichia coli BL21 (DE3) for antibiotic susceptibility determination and protein purification. Meanwhile, the purified native protein was used to determine the enzymatic activities. Results A class D β-lactamase, RAD-1, was identified in the genome of R. anatipestifer SCVM0004. It was distinct from all characterized class D β-lactamases (≤42% amino acid sequence identity). Searching in GenBank showed that blaRAD-1 was widely disseminated among R. anatipestifer. Genomic environment analysis indicated that the chromosomal structures of blaRAD-1-located regions were relatively conserved. Expression of RAD-1 in E. coli results in elevated MICs for various β-lactam antibiotics, including penicillins, extended-spectrum cephalosporins, a monobactam and carbapenems. Moreover, kinetic analysis of purified RAD-1 revealed: (i) high-level activity against penicillins; (ii) highest affinity for carbapenems; (iii) moderate hydrolysis of extended-spectrum cephalosporins and a monobactam; and (iv) no activity for oxacillin and cefoxitin. Conclusions This study identified a novel chromosomally located class D carbapenemase RAD-1 (Bush–Jacoby functional group 2def) in R. anatipestifer SCVM0004. Moreover, bioinformatic analysis confirmed that the RAD-1 was widely prevalent and conserved in R. anatipestifer.

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Section: Resultsmentioning

confidence: 99%

Identification of a novel carbapenem-hydrolysing class D β-lactamase RAD-1 inRiemerella anatipestifer

Yang

Lei

et al. 2023

Journal of Antimicrobial Chemotherapy

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“…Moreover, the phage therapeutic suitability was evaluated by PhageLeads, which analyses the phage genome for temperate genetic markers, AMR, and virulence genes. Other tools were used to further test the feasibility of the phage for therapy, including RGI Resistance Gene Identifier (RGI v5.2.1, CARD v3.2.3 ( Alcock et al., 2020 ), DBETH ( Chakraborty et al., 2012 ), and VRprofile2 ( Zankari et al., 2017 ; Bortolaia et al., 2020 ; Wang et al., 2022 ). PhageTerm (Galaxy v1.0.11) was used to predict the genome termini and packaging from sequence reads ( Garneau et al., 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Characterization and comprehensive genome analysis of novel bacteriophage, vB_Kpn_ZCKp20p, with lytic and anti-biofilm potential against clinical multidrug-resistant Klebsiella pneumoniae

Zaki

Fahmy

Aziz

et al. 2023

Front. Cell. Infect. Microbiol.

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IntroductionThe rise of infections by antibiotic-resistant bacterial pathogens is alarming. Among these, Klebsiella pneumoniae is a leading cause of death by hospital-acquired infections, and its multidrug-resistant strains are flagged as a global threat to human health, which necessitates finding novel antibiotics or alternative therapies. One promising therapeutic alternative is the use of virulent bacteriophages, which specifically target bacteria and coevolve with them to overcome potential resistance. Here, we aimed to discover specific bacteriophages with therapeutic potential against multiresistant K. pneumoniae clinical isolates.Methods and ResultsOut of six bacteriophages that we isolated from urban and medical sewage, phage vB_Kpn_ZCKp20p had the broadest host range and was thus characterized in detail. Transmission electron microscopy suggests vB_Kpn_ZCKp20p to be a tailed phage of the siphoviral morphotype. In vitro evaluation indicated a high lytic efficiency (30 min latent period and burst size of ∼100 PFU/cell), and extended stability at temperatures up to 70°C and a wide range of (2-12) pH. Additionally, phage vB_Kpn_ZCKp20p possesses antibiofilm activity that was evaluated by the crystal violet assay and was not cytotoxic to human skin fibroblasts. The whole genome was sequenced and annotated, uncovering one tRNA gene and 33 genes encoding proteins with assigned functions out of 85 predicted genes. Furthermore, comparative genomics and phylogenetic analysis suggest that vB_Kpn_ZCKp20p most likely represents a new species, but belongs to the same genus as Klebsiella phages ZCKP8 and 6691. Comprehensive genomic and bioinformatics analyses substantiate the safety of the phage and its strictly lytic lifestyle.ConclusionPhage vB_Kpn_ZCKp20p is a novel phage with potential to be used against biofilm-forming K. pneumoniae and could be a promising source for antibacterial and antibiofilm products, which will be individually studied experimentally in future studies.

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“…The non-redundant gene sequences constructed from metagenomic data were used to identify MGEs. The ORFs were aligned against corresponding databases for annotating plasmids (PLSDB, (Galata et al, 2019)), insertion sequences (ISs, ISfinder (Siguier et al, 2006)), prophages (PHASTER, (Arndt et al, 2016)), transposons (VRprofile2, (Wang et al, 2022)), integrons (INTEGRALL (Moura et al, 2009)), integrative and conjugative elements (ICEs, ICEberg 2.0 (Liu et al, 2019)), and integrative and mobilizable elements (IME, ICEberg 2.0 (Liu et al, 2019)), respectively. Moreover, a manually curated database of MGEs (mobileOG-db, (Brown et al, 2022)) was used to obtain high-quality and functional annotations.…”

Section: Methodsmentioning

confidence: 99%

Community coalescence altered the potential of horizontal gene transfers within the native soil microbiome

Liu,

Hackl,

Salles

2023

Preprint

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Microbial community coalescence, which refers to the mixing of microbial communities, frequently shapes the assemblage of soil microbiomes in natural ecosystems. It can exert selective pressure on the coalescent taxa, leading to ecological changes in microbial community structure or microbial evolutionary changes via horizontal gene transfer (HGT). However, the influence of community coalescence on the potential of HGTs within native communities, particularly in soil ecosystems, remains poorly understood. Here, we experimentally quantified the potential evolutionary consequences of soil coalescence. We achieved that by subjecting microcosms containing natural soil to invasion by several microbial communities and profiling mobile genetic elements (MGEs) and adaptive genes of microbial communities up to 60 days after coalescence. Our findings revealed both specific and common responses of MGEs to coalescences over time. Specific effects differed across invasive communities and were particularly pronounced in the early stages. Common effects were associated with an increased abundance of insertion sequences (ISs) across different treatments, suggesting that ISs played a crucial role in promoting diversification at the community level. In summary, we showed that changing MGE profiles are an intrinsic response of the soil microbial community to coalescence-imposed pressure. Our study provides new insights into the modulation of adaptability in soil microbial communities by utilizing community coalescences to address global challenges.

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VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens

Cited by 64 publications

References 30 publications

Identification of a novel carbapenem-hydrolysing class D β-lactamase RAD-1 inRiemerella anatipestifer

Identification of a novel carbapenem-hydrolysing class D β-lactamase RAD-1 inRiemerella anatipestifer

Characterization and comprehensive genome analysis of novel bacteriophage, vB_Kpn_ZCKp20p, with lytic and anti-biofilm potential against clinical multidrug-resistant Klebsiella pneumoniae

Community coalescence altered the potential of horizontal gene transfers within the native soil microbiome

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